This class stores a SRM/MRM transition. More...

#include <OpenMS/ANALYSIS/MRM/ReactionMonitoringTransition.h>

Inheritance diagram for ReactionMonitoringTransition:

Collaboration diagram for ReactionMonitoringTransition:

Classes
struct	NameLess
	Comparator by name. More...

struct	ProductMZLess
	Comparator by Product ion MZ. More...

Public Types
enum	DecoyTransitionType { UNKNOWN , TARGET , DECOY }

typedef TargetedExperimentHelper::Configuration	Configuration

typedef TargetedExperimentHelper::RetentionTime	RetentionTime

typedef TargetedExperimentHelper::TraMLProduct	Product

typedef TargetedExperimentHelper::Prediction	Prediction

Public Member Functions
Constructors and destructors
	ReactionMonitoringTransition ()
	default constructor More...

	ReactionMonitoringTransition (const ReactionMonitoringTransition &rhs)
	copy constructor More...

	ReactionMonitoringTransition (ReactionMonitoringTransition &&) noexcept
	Move constructor. More...

	~ReactionMonitoringTransition () override
	destructor More...

ReactionMonitoringTransition &	operator= (const ReactionMonitoringTransition &rhs)
	assignment operator More...

ReactionMonitoringTransition &	operator= (ReactionMonitoringTransition &&rhs)
	move assignment operator More...

Accessors
void	setName (const String &name)

const String &	getName () const

void	setNativeID (const String &name)

const String &	getNativeID () const

void	setPeptideRef (const String &peptide_ref)

const String &	getPeptideRef () const

void	setCompoundRef (const String &compound_ref)

const String &	getCompoundRef () const

void	setPrecursorMZ (double mz)
	sets the precursor mz (Q1 value) More...

double	getPrecursorMZ () const
	get the precursor mz (Q1 value) More...

bool	hasPrecursorCVTerms () const
	Returns true if precursor CV Terms exist (means it is safe to call getPrecursorCVTermList) More...

void	setPrecursorCVTermList (const CVTermList &list)

void	addPrecursorCVTerm (const CVTerm &cv_term)

const CVTermList &	getPrecursorCVTermList () const
	Obtain the list of CV Terms for the precursor. More...

void	setProductMZ (double mz)

double	getProductMZ () const

int	getProductChargeState () const

bool	isProductChargeStateSet () const

void	addProductCVTerm (const CVTerm &cv_term)

const std::vector< Product > &	getIntermediateProducts () const

void	addIntermediateProduct (Product product)

void	setIntermediateProducts (const std::vector< Product > &products)

void	setProduct (Product product)

const Product &	getProduct () const

bool	hasPrediction () const
	Returns true if a Prediction object exists (means it is safe to call getPrediction) More...

void	setPrediction (const Prediction &prediction)

void	addPredictionTerm (const CVTerm &prediction)

const Prediction &	getPrediction () const
	Obtain the Prediction object. More...

DecoyTransitionType	getDecoyTransitionType () const
	Returns the type of transition (target or decoy) More...

void	setDecoyTransitionType (const DecoyTransitionType &d)
	Sets the type of transition (target or decoy) More...

double	getLibraryIntensity () const
	Returns the library intensity (ion count or normalized ion count from a spectral library) More...

void	setLibraryIntensity (double intensity)
	Sets the library intensity (ion count or normalized ion count from a spectral library) More...

Retention time
Retention time set on transition level Note Retention time can be set on analyte level (peptide / compound level) or transition level – usually the retention time set here on transition level is ignored, therefore only use this if you have a good reason.
void	setRetentionTime (RetentionTime rt)
	Sets the retention time on transition level. More...

const RetentionTime &	getRetentionTime () const
	Gets the retention time on transition level. More...

Detecting transitions
Transitions used for detection of analyte Detecting transitions represent the set of transitions of an assay that should be used to enable candidate peak group detection. Ideally they were observed and validated in previous experiments and have an associated library intensity. For an overview, see Schubert OT et al., Building high-quality assay libraries for targeted analysis of SWATH MS data., Nat Protoc. 2015 Mar;10(3):426-41. doi: 10.1038/nprot.2015.015. Epub 2015 Feb 12. PMID: 25675208
bool	isDetectingTransition () const

void	setDetectingTransition (bool val)

Identifying transitions
Transitions used for differentiation between different analyte isomers (peptidoforms). Identifying transitions represent the set of transitions of an assay that should be used for the independent identification of a candidate peak group (often in relation to another analyte isomer or peptidoform). These transitions could for example be site-determining transitions in a phospho-proteomic DIA experiment. These transitions will be scored independently of the detecting transitions.
bool	isIdentifyingTransition () const

void	setIdentifyingTransition (bool val)

Quantifying transitions
Transitions used for quantification Quantifying transitions represent the set of transitions of an assay that should be used for the quantification of the peptide. This includes exclusion of e.g. interfered transitions (example: light/heavy peptide pairs isolated in the same swath window), that should not be used for quantification of the peptide.
bool	isQuantifyingTransition () const

void	setQuantifyingTransition (bool val)

Predicates
bool	operator== (const ReactionMonitoringTransition &rhs) const
	equality operator More...

bool	operator!= (const ReactionMonitoringTransition &rhs) const
	inequality operator More...

Public Member Functions inherited from CVTermList
	CVTermList ()=default
	Defaults constructor. More...

	CVTermList (const CVTermList &)=default
	Copy constructor. More...

	CVTermList (CVTermList &&) noexcept
	Move constructor. More...

virtual	~CVTermList ()
	Destructor. More...

CVTermList &	operator= (const CVTermList &rhs) &=default
	Assignment operator. More...

CVTermList &	operator= (CVTermList &&) &=default
	Move assignment operator. More...

void	setCVTerms (const std::vector< CVTerm > &terms)
	sets the CV terms More...

void	replaceCVTerm (const CVTerm &cv_term)
	replaces the specified CV term More...

void	replaceCVTerms (const std::vector< CVTerm > &cv_terms, const String &accession)
	replaces the specified CV terms using the given accession number More...

void	replaceCVTerms (const Map< String, std::vector< CVTerm > > &cv_term_map)
	replaces all cv terms with a map (can be obtained via getCVTerms) More...

void	consumeCVTerms (const Map< String, std::vector< CVTerm > > &cv_term_map)
	merges the given map into the member map, no duplicate checking More...

const Map< String, std::vector< CVTerm > > &	getCVTerms () const
	returns the accession string of the term More...

void	addCVTerm (const CVTerm &term)
	adds a CV term More...

bool	operator== (const CVTermList &cv_term_list) const
	equality operator More...

bool	operator!= (const CVTermList &cv_term_list) const
	inequality operator More...

bool	hasCVTerm (const String &accession) const
	checks whether the term has a value More...

bool	empty () const
	return true if no terms are available More...

Public Member Functions inherited from MetaInfoInterface
	MetaInfoInterface ()
	Constructor. More...

	MetaInfoInterface (const MetaInfoInterface &rhs)
	Copy constructor. More...

	MetaInfoInterface (MetaInfoInterface &&) noexcept
	Move constructor. More...

	~MetaInfoInterface ()
	Destructor. More...

MetaInfoInterface &	operator= (const MetaInfoInterface &rhs)
	Assignment operator. More...

MetaInfoInterface &	operator= (MetaInfoInterface &&) noexcept
	Move assignment operator. More...

bool	operator== (const MetaInfoInterface &rhs) const
	Equality operator. More...

bool	operator!= (const MetaInfoInterface &rhs) const
	Equality operator. More...

const DataValue &	getMetaValue (const String &name, const DataValue &default_value=DataValue::EMPTY) const
	Returns the value corresponding to a string, or a default value (default: DataValue::EMPTY) if not found. More...

const DataValue &	getMetaValue (UInt index, const DataValue &default_value=DataValue::EMPTY) const
	Returns the value corresponding to an index, or a default value (default: DataValue::EMPTY) if not found. More...

bool	metaValueExists (const String &name) const
	Returns whether an entry with the given name exists. More...

bool	metaValueExists (UInt index) const
	Returns whether an entry with the given index exists. More...

void	setMetaValue (const String &name, const DataValue &value)
	Sets the DataValue corresponding to a name. More...

void	setMetaValue (UInt index, const DataValue &value)
	Sets the DataValue corresponding to an index. More...

void	removeMetaValue (const String &name)
	Removes the DataValue corresponding to `name` if it exists. More...

void	removeMetaValue (UInt index)
	Removes the DataValue corresponding to `index` if it exists. More...

void	addMetaValues (const MetaInfoInterface &from)
	function to copy all meta values from one object to this one More...

void	getKeys (std::vector< String > &keys) const
	Fills the given vector with a list of all keys for which a value is set. More...

void	getKeys (std::vector< UInt > &keys) const
	Fills the given vector with a list of all keys for which a value is set. More...

bool	isMetaEmpty () const
	Returns if the MetaInfo is empty. More...

void	clearMetaInfo ()
	Removes all meta values. More...

Protected Member Functions
Comparator classes.
These classes implement binary predicates that can be used to compare two transitions with respect to their name.
void	updateMembers_ ()

Protected Member Functions inherited from MetaInfoInterface
void	createIfNotExists_ ()
	Creates the MetaInfo object if it does not exist. More...

Protected Attributes
Attributes
String	name_
	id, required attribute More...

String	peptide_ref_
	Reference to a specific peptide. More...

String	compound_ref_
	Reference to a specific compound. More...

double	library_intensity_
	Intensity of the product (q3) ion (stored in CV Term 1001226 inside the <Transition> tag) More...

DecoyTransitionType	decoy_type_
	specific properties of a transition (e.g. specific CV terms) More...

Subelements
double	precursor_mz_
	A transition has exactly one precursor and it must supply the CV Term 1000827 (isolation window target m/z) More...

CVTermList *	precursor_cv_terms_
	(Other) CV Terms of the Precursor (Q1) of the transition or target More...

Product	product_
	Product (Q3) of the transition. More...

std::vector< Product >	intermediate_products_
	Intermediate product ion information of the transition when using MS3 or above (optional) More...

RetentionTime	rts
	Information about predicted or calibrated retention time (optional) More...

Prediction *	prediction_
	Information about a prediction for a suitable transition using some software (optional) More...

std::bitset< 3 >	transition_flags_

Protected Attributes inherited from CVTermList
Map< String, std::vector< CVTerm > >	cv_terms_

Protected Attributes inherited from MetaInfoInterface
MetaInfo *	meta_
	Pointer to the MetaInfo object (0 by default) More...

Additional Inherited Members
Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistry &	metaRegistry ()
	Returns a reference to the MetaInfoRegistry. More...

Detailed Description

This class stores a SRM/MRM transition.

This class is capable of representing a <Transition> tag in a TraML document completely and contains all associated information.

The default values for precursor m/z is 0.0 which indicates that it is uninitialized.

Member Typedef Documentation

◆ Configuration

typedef TargetedExperimentHelper::Configuration Configuration

◆ Prediction

typedef TargetedExperimentHelper::Prediction Prediction

◆ Product

typedef TargetedExperimentHelper::TraMLProduct Product

◆ RetentionTime

typedef TargetedExperimentHelper::RetentionTime RetentionTime

Member Enumeration Documentation

◆ DecoyTransitionType

enum DecoyTransitionType

Enumerator
UNKNOWN	Unknown type.
TARGET	Target transition.
DECOY	Decoy transition.

Constructor & Destructor Documentation

◆ ReactionMonitoringTransition() [1/3]

ReactionMonitoringTransition ( )

default constructor

◆ ReactionMonitoringTransition() [2/3]

ReactionMonitoringTransition ( const ReactionMonitoringTransition & rhs )

copy constructor

◆ ReactionMonitoringTransition() [3/3]

ReactionMonitoringTransition ( ReactionMonitoringTransition && )

noexcept

Move constructor.

◆ ~ReactionMonitoringTransition()

~ReactionMonitoringTransition ( )

override

destructor

Member Function Documentation

◆ addIntermediateProduct()

void addIntermediateProduct ( Product product )

◆ addPrecursorCVTerm()

void addPrecursorCVTerm ( const CVTerm & cv_term )

◆ addPredictionTerm()

void addPredictionTerm ( const CVTerm & prediction )

◆ addProductCVTerm()

void addProductCVTerm ( const CVTerm & cv_term )

◆ getCompoundRef()

const String& getCompoundRef ( ) const

Referenced by ChromatogramExtractor::prepareSpectra_().

◆ getDecoyTransitionType()

DecoyTransitionType getDecoyTransitionType ( ) const

Returns the type of transition (target or decoy)

◆ getIntermediateProducts()

const std::vector<Product>& getIntermediateProducts ( ) const

◆ getLibraryIntensity()

double getLibraryIntensity ( ) const

Returns the library intensity (ion count or normalized ion count from a spectral library)

◆ getName()

const String& getName ( ) const

Referenced by ReactionMonitoringTransition::NameLess::operator()().

◆ getNativeID()

const String& getNativeID ( ) const

Referenced by ChromatogramExtractor::prepareSpectra_().

◆ getPeptideRef()

const String& getPeptideRef ( ) const

Referenced by ChromatogramExtractor::prepareSpectra_().

◆ getPrecursorCVTermList()

const CVTermList& getPrecursorCVTermList ( ) const

Obtain the list of CV Terms for the precursor.

Note: You first need to check whether they exist using hasPrecursorCVTerms()

◆ getPrecursorMZ()

double getPrecursorMZ ( ) const

get the precursor mz (Q1 value)

Referenced by ChromatogramExtractor::prepareSpectra_().

◆ getPrediction()

const Prediction& getPrediction ( ) const

Obtain the Prediction object.

Note: You first need to check whether the object is accessible using hasPrediction()

◆ getProduct()

const Product& getProduct ( ) const

◆ getProductChargeState()

int getProductChargeState ( ) const

◆ getProductMZ()

double getProductMZ ( ) const

Referenced by ReactionMonitoringTransition::ProductMZLess::operator()(), and ChromatogramExtractor::prepareSpectra_().

◆ getRetentionTime()

const RetentionTime& getRetentionTime ( ) const

Gets the retention time on transition level.

Stores a retention time on the level of an individual transition

Note: This is very likely not what you want, to set the retention time of an analyte use TargetedExperimentHelper::PeptideCompound::getRetentionTime()

◆ hasPrecursorCVTerms()

bool hasPrecursorCVTerms ( ) const

Returns true if precursor CV Terms exist (means it is safe to call getPrecursorCVTermList)

◆ hasPrediction()

bool hasPrediction ( ) const

Returns true if a Prediction object exists (means it is safe to call getPrediction)

◆ isDetectingTransition()

bool isDetectingTransition ( ) const

◆ isIdentifyingTransition()

bool isIdentifyingTransition ( ) const

◆ isProductChargeStateSet()

bool isProductChargeStateSet ( ) const

◆ isQuantifyingTransition()

bool isQuantifyingTransition ( ) const

◆ operator!=()

bool operator!= ( const ReactionMonitoringTransition & rhs ) const

inequality operator

◆ operator=() [1/2]

ReactionMonitoringTransition& operator= ( const ReactionMonitoringTransition & rhs )

assignment operator

◆ operator=() [2/2]

ReactionMonitoringTransition& operator= ( ReactionMonitoringTransition && rhs )

move assignment operator

◆ operator==()

bool operator== ( const ReactionMonitoringTransition & rhs ) const

equality operator

◆ setCompoundRef()

void setCompoundRef ( const String & compound_ref )

◆ setDecoyTransitionType()

void setDecoyTransitionType ( const DecoyTransitionType & d )

Sets the type of transition (target or decoy)

◆ setDetectingTransition()

void setDetectingTransition ( bool val )

◆ setIdentifyingTransition()

void setIdentifyingTransition ( bool val )

◆ setIntermediateProducts()

void setIntermediateProducts ( const std::vector< Product > & products )

◆ setLibraryIntensity()

void setLibraryIntensity ( double intensity )

Sets the library intensity (ion count or normalized ion count from a spectral library)

◆ setName()

void setName ( const String & name )

◆ setNativeID()

void setNativeID ( const String & name )

◆ setPeptideRef()

void setPeptideRef ( const String & peptide_ref )

◆ setPrecursorCVTermList()

void setPrecursorCVTermList ( const CVTermList & list )

◆ setPrecursorMZ()

void setPrecursorMZ ( double mz )

sets the precursor mz (Q1 value)

◆ setPrediction()

void setPrediction ( const Prediction & prediction )

◆ setProduct()

void setProduct ( Product product )

◆ setProductMZ()

void setProductMZ ( double mz )

◆ setQuantifyingTransition()

void setQuantifyingTransition ( bool val )

◆ setRetentionTime()

void setRetentionTime ( RetentionTime rt )

Sets the retention time on transition level.

Stores a retention time on the level of an individual transition

Note: This is very likely not what you want, to set the retention time of an analyte use TargetedExperimentHelper::PeptideCompound::getRetentionTime()

◆ updateMembers_()

void updateMembers_ ( )

protected

Member Data Documentation

◆ compound_ref_

String compound_ref_

protected

Reference to a specific compound.

◆ decoy_type_

DecoyTransitionType decoy_type_

protected

specific properties of a transition (e.g. specific CV terms)

◆ intermediate_products_

std::vector<Product> intermediate_products_

protected

Intermediate product ion information of the transition when using MS3 or above (optional)

◆ library_intensity_

double library_intensity_

protected

Intensity of the product (q3) ion (stored in CV Term 1001226 inside the <Transition> tag)

◆ name_

String name_

protected

id, required attribute

◆ peptide_ref_

String peptide_ref_

protected

Reference to a specific peptide.

◆ precursor_cv_terms_

CVTermList* precursor_cv_terms_

protected

(Other) CV Terms of the Precursor (Q1) of the transition or target

◆ precursor_mz_

double precursor_mz_

protected

A transition has exactly one precursor and it must supply the CV Term 1000827 (isolation window target m/z)

◆ prediction_

Prediction* prediction_

protected

Information about a prediction for a suitable transition using some software (optional)

◆ product_

Product product_

protected

Product (Q3) of the transition.

◆ rts

RetentionTime rts

protected

Information about predicted or calibrated retention time (optional)

◆ transition_flags_

std::bitset<3> transition_flags_

protected

A set of flags to store information about the transition at hand (currently: detecting, identifying and quantifying)

Classes

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Configuration

◆ Prediction

◆ Product

◆ RetentionTime

Member Enumeration Documentation

◆ DecoyTransitionType

Constructor & Destructor Documentation

◆ ReactionMonitoringTransition() [1/3]

◆ ReactionMonitoringTransition() [2/3]

◆ ReactionMonitoringTransition() [3/3]

◆ ~ReactionMonitoringTransition()

Member Function Documentation

◆ addIntermediateProduct()

◆ addPrecursorCVTerm()

◆ addPredictionTerm()

◆ addProductCVTerm()

◆ getCompoundRef()

◆ getDecoyTransitionType()

◆ getIntermediateProducts()

◆ getLibraryIntensity()

◆ getName()

◆ getNativeID()

◆ getPeptideRef()

◆ getPrecursorCVTermList()

◆ getPrecursorMZ()

◆ getPrediction()

◆ getProduct()

◆ getProductChargeState()

◆ getProductMZ()

◆ getRetentionTime()

◆ hasPrecursorCVTerms()

◆ hasPrediction()

◆ isDetectingTransition()

◆ isIdentifyingTransition()

◆ isProductChargeStateSet()

◆ isQuantifyingTransition()

◆ operator!=()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator==()

◆ setCompoundRef()

◆ setDecoyTransitionType()

◆ setDetectingTransition()

◆ setIdentifyingTransition()

◆ setIntermediateProducts()

◆ setLibraryIntensity()

◆ setName()

◆ setNativeID()

◆ setPeptideRef()

◆ setPrecursorCVTermList()

◆ setPrecursorMZ()

◆ setPrediction()

◆ setProduct()

◆ setProductMZ()

◆ setQuantifyingTransition()

◆ setRetentionTime()

◆ updateMembers_()

Member Data Documentation

◆ compound_ref_

◆ decoy_type_

◆ intermediate_products_

◆ library_intensity_

◆ name_

◆ peptide_ref_

◆ precursor_cv_terms_

◆ precursor_mz_

◆ prediction_

◆ product_

◆ rts

◆ transition_flags_